GgaINT1020565 @ galGal4
Intron Retention
Gene
ENSGALG00000014450 | PABPC1
Description
polyadenylate-binding protein 1 [Source:RefSeq peptide;Acc:NP_001026768]
Coordinates
chr2:128376372-128376768:-
Coord C1 exon
chr2:128376684-128376768
Coord A exon
chr2:128376503-128376683
Coord C2 exon
chr2:128376372-128376502
Length
181 bp
Sequences
Splice sites
5' ss Seq
TAGGTATGT
5' ss Score
7.76
3' ss Seq
GATAACGTTTTTCTCTCTAGGTG
3' ss Score
11.83
Exon sequences
Seq C1 exon
CCTGCTGTCCATGTGCAAGGCCAGGAACCCTTGACTGCTTCCATGTTGGCTTCTGCCCCTCCACAAGAACAAAAGCAGATGTTAG
Seq A exon
GTATGTACATGGCATCTTTATGTCTTGCAGAAGTATGCTGAGTACTCTATTACTAATCTTAAAATACATAGTAAATGGTTTTCAGGGTGGAACAAGGAGACTTGTGTTGCTCTTTTTCCTTGAATCTAGGCTATGCTCATCAGATGAGATTTCTCACTCCAGATAACGTTTTTCTCTCTAG
Seq C2 exon
GTGAACGTCTATTTCCTCTTATTCAAAGCATGCACCCTACTCTGGCGGGTAAGATCACTGGTATGTTATTGGAGATTGACAACTCTGAACTCCTTCACATGCTCGAGTCTCCTGAGTCTCTTCGTTCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000014450:ENSGALT00000023333:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.364
Domain overlap (PFAM):
C1:
PF0065813=PABP=PU(27.8=69.0)
A:
NA
C2:
PF0065813=PABP=FE(59.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGTCCATGTGCAAGGCCAG
R:
TCGAACGAAGAGACTCAGGAGA
Band lengths:
210-391
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]